11-111783896-CTATAT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_024740.2(ALG9):c.*2496_*2500del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (5296 hom., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: ALG9 NM_024740.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.28

Genes affected

ALG9 (HGNC:15672): (ALG9 alpha-1,2-mannosyltransferase) This gene encodes an alpha-1,2-mannosyltransferase enzyme that functions in lipid-linked oligosaccharide assembly. Mutations in this gene result in congenital disorder of glycosylation type Il. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-111783896-CTATAT-C is Benign according to our data. Variant chr11-111783896-CTATAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 302379.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALG9	NM_024740.2	c.*2496_*2500del		3_prime_UTR_variant	15/15	ENST00000616540.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG9	ENST00000616540.5	c.*2496_*2500del		3_prime_UTR_variant	15/15	1	NM_024740.2
ALG9	ENST00000532425.6	c.*2156_*2160del		3_prime_UTR_variant	6/6	3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 38960 AN: 148562 Hom.: 5297 Cov.: 19

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.302

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.300

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.262 AC: 38965 AN: 148666 Hom.: 5296 Cov.: 19 AF XY: 0.262 AC XY: 18965 AN XY: 72348

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.297

Alfa AF: 0.252 Hom.: 539

Asia WGS AF: 0.211 AC: 729 AN: 3450

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital disorder of glycosylation Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3833761; hg19: chr11-111654620;